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bio-pipeline

My collection of light bioinformatics analysis pipelines for specific tasks

bioinformatica

Pipelines e scripts para análise de Bioinformática

bioinformatics-scripts

Repository for Bioinformatics scripts and basic programs developed by L.M.C

davincicode

Collection of all scripts and try-out scripts

fieldimager

FIELDimageR: A R package to analyze orthomosaic images from agricultural field trials. This package is a compilation of functions to analyze pos-mosaicking images from research fields, and allows to: crop the image; remove soil effect; build vegetation indices; rotate the image; build the plot shapefile; extract information for each plot; and evaluate stand count, canopy percentage, and plant height.

flavonoidfriday

Flavonoids are specialized metabolites in plants that have numerous functions including protection against abiotic stresses, pigmentation, and repelling herbivores.This repository provides additional background to the #FlavonoidFriday tweets

gaas

Genome Assembly and Annotation Service code

genome_skimming_utilities

gtf_fixer_to_gffread

Script to replace end positions of a GTF file with the sequence size of a single line FASTA file.

gwdsr

Wrapper scripts for an integrative analysis workflow for genome-wide detection of selection and recombination

hyphy

HyPhy: Hypothesis testing using Phylogenies

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

kentutils

UCSC command line bioinformatic utilities

lactad-bioinfo-2013

Exercícios de Perl em Bioinformática - Curso de Bioinformática LaCTAD Unicamp 2013

lskscripts

A placeholder for all my random scripts. Some scripts might eventually graduate and go to their own projects, so don't be surprised if anything leaves in the future.

manuscripts

orthofinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

perlscripts

some small perl scripts

perlscripts_jit

All the misc. perl scripts

pirate

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)

quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

scripts

General scripts used in the lab. Almost all of them are in core perl, i.e require no modules that don't already come with a perl installation. These script are currently in use by the Lab, so expect full support. This material is based upon work supported by the National Science Foundation under Grant Number EAR-1035955. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

vcfhunter